1. Some people use screw shafts (it's just a pole with a screw in the end) and they just secure it inside the case and use the screw to hold it together or you could use little plastic tabs along the edge of the case with screws to hold it in place (the first method is a little more reliable but takes up more space).
2. A fan isn't something that you need but it's always nice to have, if you have replaced the heat sinks with copper ones and have good ventilation on the case then I would say you don't need one.
3. There are 2 ways to mount the controls for you portable, you can cut you the button holes from the controller you are using and cement them into the case using bondo and then use the screw shafts that came with the button holes to hold the buttons securely in place or you could get a bunch of momentary contact buttons from radioshack and just drill hole in the case and drop them in and use the bolt to secure them from the back and then you just solder the two leads to ground and to what ever button you want on the controller board.
4. If you are using a psone screen, the case comes with screw shafts to mount it securely in place, the n64 mobo has mounting holes on the sides which you could just fashion some pegs to hold that in place and the controller board weighs barely anything so you could just use some electrical tape to hold it to the case.
Hope that helps